niwrap-freesurfer 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/meanval.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MEANVAL_METADATA = Metadata(
-    id="6d7fa2eae6c9b81ace8c569ec0e5ab41bead6351.boutiques",
+    id="26ed631dfd8a79a0f878fcf7adc5c3c7373c6d16.boutiques",
     name="meanval",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MEANVAL_METADATA = Metadata(
 
 
 MeanvalParameters = typing.TypedDict('MeanvalParameters', {
-    "__STYXTYPE__": typing.Literal["meanval"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/meanval"]],
+    "input_file": InputPathType,
+    "mask_file": InputPathType,
+    "output_file": str,
+    "avgwf_flag": bool,
+})
+MeanvalParametersTagged = typing.TypedDict('MeanvalParametersTagged', {
+    "@type": typing.Literal["freesurfer/meanval"],
     "input_file": InputPathType,
     "mask_file": InputPathType,
     "output_file": str,
     "avgwf_flag": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "meanval": meanval_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "meanval": meanval_outputs,
-    }.get(t)
 
 
 class MeanvalOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `meanval(...)`.
+    Output object returned when calling `MeanvalParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def meanval_params(
     mask_file: InputPathType,
     output_file: str,
     avgwf_flag: bool = False,
-) -> MeanvalParameters:
+) -> MeanvalParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def meanval_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "meanval",
+        "@type": "freesurfer/meanval",
         "input_file": input_file,
         "mask_file": mask_file,
         "output_file": output_file,
@@ -108,17 +83,17 @@ def meanval_cargs(
     cargs.append("meanval")
     cargs.extend([
         "--i",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
     cargs.extend([
         "--m",
-        execution.input_file(params.get("mask_file"))
+        execution.input_file(params.get("mask_file", None))
     ])
     cargs.extend([
         "--o",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
-    if params.get("avgwf_flag"):
+    if params.get("avgwf_flag", False):
         cargs.append("--avgwf")
     return cargs
 
@@ -138,16 +113,18 @@ def meanval_outputs(
     """
     ret = MeanvalOutputs(
         root=execution.output_file("."),
-        mean_output_file=execution.output_file(params.get("output_file")),
+        mean_output_file=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def meanval_execute(
     params: MeanvalParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MeanvalOutputs:
     """
+    meanval
+    
     Tool to calculate the mean value of an image within a mask.
     
     Author: FreeSurfer Developers
@@ -156,10 +133,12 @@ def meanval_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MeanvalOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MEANVAL_METADATA)
     params = execution.params(params)
     cargs = meanval_cargs(params, execution)
     ret = meanval_outputs(params, execution)
@@ -175,6 +154,8 @@ def meanval(
     runner: Runner | None = None,
 ) -> MeanvalOutputs:
     """
+    meanval
+    
     Tool to calculate the mean value of an image within a mask.
     
     Author: FreeSurfer Developers
@@ -190,21 +171,19 @@ def meanval(
     Returns:
         NamedTuple of outputs (described in `MeanvalOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MEANVAL_METADATA)
     params = meanval_params(
         input_file=input_file,
         mask_file=mask_file,
         output_file=output_file,
         avgwf_flag=avgwf_flag,
     )
-    return meanval_execute(params, execution)
+    return meanval_execute(params, runner)
 
 
 __all__ = [
     "MEANVAL_METADATA",
     "MeanvalOutputs",
-    "MeanvalParameters",
     "meanval",
+    "meanval_execute",
     "meanval_params",
 ]

niwrap_freesurfer/freesurfer/merge_stats_tables.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MERGE_STATS_TABLES_METADATA = Metadata(
-    id="75cd0efd4969a80f33c93957c7f3deb75c32e6cc.boutiques",
+    id="d8d350b7070bfceef10a5f231b3451eeeaa849f2.boutiques",
     name="merge_stats_tables",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,25 @@ MERGE_STATS_TABLES_METADATA = Metadata(
 
 
 MergeStatsTablesParameters = typing.TypedDict('MergeStatsTablesParameters', {
-    "__STYXTYPE__": typing.Literal["merge_stats_tables"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/merge_stats_tables"]],
+    "subjects": typing.NotRequired[list[str] | None],
+    "subject": typing.NotRequired[str | None],
+    "subjectsfile": typing.NotRequired[InputPathType | None],
+    "inputs": typing.NotRequired[list[InputPathType] | None],
+    "input": typing.NotRequired[InputPathType | None],
+    "outputfile": str,
+    "meas": str,
+    "common_segs": bool,
+    "all_segs": bool,
+    "intable": typing.NotRequired[InputPathType | None],
+    "subdir": typing.NotRequired[str | None],
+    "delimiter": typing.NotRequired[str | None],
+    "transpose": bool,
+    "skip": bool,
+    "debug": bool,
+})
+MergeStatsTablesParametersTagged = typing.TypedDict('MergeStatsTablesParametersTagged', {
+    "@type": typing.Literal["freesurfer/merge_stats_tables"],
     "subjects": typing.NotRequired[list[str] | None],
     "subject": typing.NotRequired[str | None],
     "subjectsfile": typing.NotRequired[InputPathType | None],
@@ -31,43 +49,11 @@ MergeStatsTablesParameters = typing.TypedDict('MergeStatsTablesParameters', {
     "skip": bool,
     "debug": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "merge_stats_tables": merge_stats_tables_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "merge_stats_tables": merge_stats_tables_outputs,
-    }.get(t)
 
 
 class MergeStatsTablesOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `merge_stats_tables(...)`.
+    Output object returned when calling `MergeStatsTablesParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -91,7 +77,7 @@ def merge_stats_tables_params(
     transpose: bool = False,
     skip: bool = False,
     debug: bool = False,
-) -> MergeStatsTablesParameters:
+) -> MergeStatsTablesParametersTagged:
     """
     Build parameters.
     
@@ -121,7 +107,7 @@ def merge_stats_tables_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "merge_stats_tables",
+        "@type": "freesurfer/merge_stats_tables",
         "outputfile": outputfile,
         "meas": meas,
         "common_segs": common_segs,
@@ -164,63 +150,63 @@ def merge_stats_tables_cargs(
     """
     cargs = []
     cargs.append("merge_stats_tables")
-    if params.get("subjects") is not None:
+    if params.get("subjects", None) is not None:
         cargs.extend([
             "--subjects",
-            *params.get("subjects")
+            *params.get("subjects", None)
         ])
-    if params.get("subject") is not None:
+    if params.get("subject", None) is not None:
         cargs.extend([
             "-s",
-            params.get("subject")
+            params.get("subject", None)
         ])
-    if params.get("subjectsfile") is not None:
+    if params.get("subjectsfile", None) is not None:
         cargs.extend([
             "--subjectsfile",
-            execution.input_file(params.get("subjectsfile"))
+            execution.input_file(params.get("subjectsfile", None))
         ])
-    if params.get("inputs") is not None:
+    if params.get("inputs", None) is not None:
         cargs.extend([
             "--inputs",
-            *[execution.input_file(f) for f in params.get("inputs")]
+            *[execution.input_file(f) for f in params.get("inputs", None)]
         ])
-    if params.get("input") is not None:
+    if params.get("input", None) is not None:
         cargs.extend([
             "-i",
-            execution.input_file(params.get("input"))
+            execution.input_file(params.get("input", None))
         ])
     cargs.extend([
         "-t",
-        params.get("outputfile")
+        params.get("outputfile", None)
     ])
     cargs.extend([
         "-m",
-        params.get("meas")
+        params.get("meas", None)
     ])
-    if params.get("common_segs"):
+    if params.get("common_segs", False):
         cargs.append("--common-segs")
-    if params.get("all_segs"):
+    if params.get("all_segs", False):
         cargs.append("--all-segs")
-    if params.get("intable") is not None:
+    if params.get("intable", None) is not None:
         cargs.extend([
             "--intable",
-            execution.input_file(params.get("intable"))
+            execution.input_file(params.get("intable", None))
         ])
-    if params.get("subdir") is not None:
+    if params.get("subdir", None) is not None:
         cargs.extend([
             "--subdir",
-            params.get("subdir")
+            params.get("subdir", None)
         ])
-    if params.get("delimiter") is not None:
+    if params.get("delimiter", None) is not None:
         cargs.extend([
             "-d",
-            params.get("delimiter")
+            params.get("delimiter", None)
         ])
-    if params.get("transpose"):
+    if params.get("transpose", False):
         cargs.append("--transpose")
-    if params.get("skip"):
+    if params.get("skip", False):
         cargs.append("--skip")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-v")
     return cargs
 
@@ -240,18 +226,20 @@ def merge_stats_tables_outputs(
     """
     ret = MergeStatsTablesOutputs(
         root=execution.output_file("."),
-        merged_stats_table=execution.output_file(params.get("outputfile")),
+        merged_stats_table=execution.output_file(params.get("outputfile", None)),
     )
     return ret
 
 
 def merge_stats_tables_execute(
     params: MergeStatsTablesParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MergeStatsTablesOutputs:
     """
-    Merges a set of stats table files into a single stats table where each line is a
-    subject and each column is a segmentation or parcellation.
+    merge_stats_tables
+    
+    Merges a set of stats table files into a single stats table where each line
+    is a subject and each column is a segmentation or parcellation.
     
     Author: FreeSurfer Developers
     
@@ -259,10 +247,12 @@ def merge_stats_tables_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MergeStatsTablesOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MERGE_STATS_TABLES_METADATA)
     params = execution.params(params)
     cargs = merge_stats_tables_cargs(params, execution)
     ret = merge_stats_tables_outputs(params, execution)
@@ -289,8 +279,10 @@ def merge_stats_tables(
     runner: Runner | None = None,
 ) -> MergeStatsTablesOutputs:
     """
-    Merges a set of stats table files into a single stats table where each line is a
-    subject and each column is a segmentation or parcellation.
+    merge_stats_tables
+    
+    Merges a set of stats table files into a single stats table where each line
+    is a subject and each column is a segmentation or parcellation.
     
     Author: FreeSurfer Developers
     
@@ -322,8 +314,6 @@ def merge_stats_tables(
     Returns:
         NamedTuple of outputs (described in `MergeStatsTablesOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MERGE_STATS_TABLES_METADATA)
     params = merge_stats_tables_params(
         subjects=subjects,
         subject=subject,
@@ -341,13 +331,13 @@ def merge_stats_tables(
         skip=skip,
         debug=debug,
     )
-    return merge_stats_tables_execute(params, execution)
+    return merge_stats_tables_execute(params, runner)
 
 
 __all__ = [
     "MERGE_STATS_TABLES_METADATA",
     "MergeStatsTablesOutputs",
-    "MergeStatsTablesParameters",
     "merge_stats_tables",
+    "merge_stats_tables_execute",
     "merge_stats_tables_params",
 ]

niwrap_freesurfer/freesurfer/mergeseg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MERGESEG_METADATA = Metadata(
-    id="624a69773d36ee5f8c473ad56e85306f6dfa8dd3.boutiques",
+    id="c13fa35219d8f22307e0e12231dd7d64c0be3c71.boutiques",
     name="mergeseg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ MERGESEG_METADATA = Metadata(
 
 
 MergesegParameters = typing.TypedDict('MergesegParameters', {
-    "__STYXTYPE__": typing.Literal["mergeseg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mergeseg"]],
+    "src_seg": InputPathType,
+    "merge_seg": InputPathType,
+    "out_seg": str,
+    "segid": typing.NotRequired[float | None],
+    "segid_only": typing.NotRequired[float | None],
+    "segid_erode": typing.NotRequired[float | None],
+    "ctab": typing.NotRequired[InputPathType | None],
+})
+MergesegParametersTagged = typing.TypedDict('MergesegParametersTagged', {
+    "@type": typing.Literal["freesurfer/mergeseg"],
     "src_seg": InputPathType,
     "merge_seg": InputPathType,
     "out_seg": str,
@@ -23,43 +33,11 @@ MergesegParameters = typing.TypedDict('MergesegParameters', {
     "segid_erode": typing.NotRequired[float | None],
     "ctab": typing.NotRequired[InputPathType | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mergeseg": mergeseg_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "mergeseg": mergeseg_outputs,
-    }.get(t)
 
 
 class MergesegOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mergeseg(...)`.
+    Output object returned when calling `MergesegParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def mergeseg_params(
     segid_only: float | None = None,
     segid_erode: float | None = None,
     ctab: InputPathType | None = None,
-) -> MergesegParameters:
+) -> MergesegParametersTagged:
     """
     Build parameters.
     
@@ -93,7 +71,7 @@ def mergeseg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mergeseg",
+        "@type": "freesurfer/mergeseg",
         "src_seg": src_seg,
         "merge_seg": merge_seg,
         "out_seg": out_seg,
@@ -124,31 +102,31 @@ def mergeseg_cargs(
     """
     cargs = []
     cargs.append("mergeseg")
-    cargs.append(execution.input_file(params.get("src_seg")))
-    cargs.append(execution.input_file(params.get("merge_seg")))
+    cargs.append(execution.input_file(params.get("src_seg", None)))
+    cargs.append(execution.input_file(params.get("merge_seg", None)))
     cargs.extend([
         "--o",
-        params.get("out_seg")
+        params.get("out_seg", None)
     ])
-    if params.get("segid") is not None:
+    if params.get("segid", None) is not None:
         cargs.extend([
             "--segid",
-            str(params.get("segid"))
+            str(params.get("segid", None))
         ])
-    if params.get("segid_only") is not None:
+    if params.get("segid_only", None) is not None:
         cargs.extend([
             "--segid-only",
-            str(params.get("segid_only"))
+            str(params.get("segid_only", None))
         ])
-    if params.get("segid_erode") is not None:
+    if params.get("segid_erode", None) is not None:
         cargs.extend([
             "--segid-erode",
-            str(params.get("segid_erode"))
+            str(params.get("segid_erode", None))
         ])
-    if params.get("ctab") is not None:
+    if params.get("ctab", None) is not None:
         cargs.extend([
             "--ctab",
-            execution.input_file(params.get("ctab"))
+            execution.input_file(params.get("ctab", None))
         ])
     return cargs
 
@@ -168,16 +146,18 @@ def mergeseg_outputs(
     """
     ret = MergesegOutputs(
         root=execution.output_file("."),
-        output_seg=execution.output_file(params.get("out_seg")),
+        output_seg=execution.output_file(params.get("out_seg", None)),
     )
     return ret
 
 
 def mergeseg_execute(
     params: MergesegParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MergesegOutputs:
     """
+    mergeseg
+    
     Merges one segmentation into another, replacing the source voxels with those
     from the merge segmentation where non-zero.
     
@@ -187,10 +167,12 @@ def mergeseg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MergesegOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MERGESEG_METADATA)
     params = execution.params(params)
     cargs = mergeseg_cargs(params, execution)
     ret = mergeseg_outputs(params, execution)
@@ -209,6 +191,8 @@ def mergeseg(
     runner: Runner | None = None,
 ) -> MergesegOutputs:
     """
+    mergeseg
+    
     Merges one segmentation into another, replacing the source voxels with those
     from the merge segmentation where non-zero.
     
@@ -230,8 +214,6 @@ def mergeseg(
     Returns:
         NamedTuple of outputs (described in `MergesegOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MERGESEG_METADATA)
     params = mergeseg_params(
         src_seg=src_seg,
         merge_seg=merge_seg,
@@ -241,13 +223,13 @@ def mergeseg(
         segid_erode=segid_erode,
         ctab=ctab,
     )
-    return mergeseg_execute(params, execution)
+    return mergeseg_execute(params, runner)
 
 
 __all__ = [
     "MERGESEG_METADATA",
     "MergesegOutputs",
-    "MergesegParameters",
     "mergeseg",
+    "mergeseg_execute",
     "mergeseg_params",
 ]